- What are they?
- What are they good for?
- How do I use them?
Definition: a network in which has two sets of nodes with edges between and not within sets.
http://mangal.uqar.ca/doc/spec/
http://biorxiv.org/content/biorxiv/early/2015/02/24/002634.full.pdf
Can you represent your network as two distinct sets?
2+2
## [1] 4
four = 2 + 2
four = 2 + 2 print(four)
## [1] 4
library(bipartite)
Import/Load models using read.csv
people.fas.harvard.edu/~matthewklau/bipmodel.csv
our.binet <- read.csv('../data/bipmodel.csv')
binet.nest <- nestedness(our.binet,null.models=FALSE) names(binet.nest) binet.nest$temperature
binet.nest <- nestedness(our.binet,null.models=TRUE,n.nulls=10)
plotweb(our.binet)
binet.mods <- computeModules(our.binet)
binet.mods
plotModuleWeb(binet.mods)
null.nets <- nullmodel(our.binet, N=1000, method="r2d")
null.mods <- lapply(null.nets,computeModules)
null.mods <- lapply(null.mods,slot,name='likelihood')
Caclulate z-value and p-value for right-tailed test:
obs.mods <- slot(obs.mods,name='likelihood')
null.mods <- unlist(null.mods)
z.val <- (obs.mods - mean(null.mods)) / sd(null.mods) z.val
## [1] 24.52201
p.val <- length(null.mods[null.mods >= obs.mods]) / length(null.mods) p.val
## [1] 0
Bascompte J. and Jordano P. 2014. Mutualistic networks. Prineton University Press.
Fortuna M.A. et al. 2010. Nestedness versus modularity in ecological networks: two sides of the same coin?. J. Anim. Ecol., 7:811-817.
Gotelli N.J. and Ellison A.M. 2013. Primer of Ecological Statistics. Sinauer Associates, Inc.
Bluthgen N. et al. 2008. What do interaction network metrics tell us about specialization and biological traits?. Ecology, 89: 3387-3399.
Fontaine et al. 2011. Stability of ecological communities and the architecture of mutualistic and trophic networks. Ecol. Lett., 14: 1170-1181.
Other Network Packages
This function will right a network class model to a text file formatted for EcoNet.
data(oyster) write.EcoNet(oyster,file='./oyster.txt',mn='ena_model_oyster')